New sources and instrumentation for neutrons in biology

Nanoscopic lipid domains determined by microscopy and neutron scattering

Biological membranes are highly complex supramolecular assemblies, which play central roles in biology. However, their complexity makes them challenging to study their nanoscale structures. To overcome this challenge, model membranes assembled using reduced sets of membrane-associated biomolecules have been found to be both excellent and tractable proxies for biological membranes. Due to their relative simplicity, they have been studied using a range of biophysical characterization techniques. In this review article, we will briefly detail the use of fluorescence and electron microscopies, and X-ray and neutron scattering techniques used over the past few decades to study the nanostructure of biological membranes.

Optimizing Crystal Size of Photosystem II by Macroseeding: Toward Neutron Protein Crystallography

Photosystem II (PSII) catalyzes the photo-oxidation of water to molecular oxygen and protons. The water splitting reaction occurs inside the oxygen-evolving complex (OEC) via a Mn₄CaO₅ cluster. To elucidate the reaction mechanism, detailed structural information for each intermediate state of the OEC is required. Despite the current high-resolution crystal structure of PSII at 1.85 Å and other efforts to follow the structural changes of the Mn₄CaO₅ cluster using X-ray free electron laser (XFEL) crystallography in addition to spectroscopic methods, many details about the reaction mechanism and conformational changes in the catalytic site during water oxidation still remain elusive. In this study, we present a rarely found successful application of the conventional macroseeding method to a large membrane protein like the dimeric PSII core complex (dPSIIcc). Combining microseeding with macroseeding crystallization techniques allowed us to reproducibly grow large dPSIIcc crystals with a size of ~3 mm. These large crystals will help improve the data collected from spectroscopic methods like polarized extended X-ray absorption fine structure (EXAFS) and single crystal electron paramagnetic resonance (EPR) techniques and are a prerequisite for determining a three-dimensional structure using neutron diffraction.

Future directions in high-pressure neutron diffraction

The ability to manipulate structure and properties using pressure has been well known for many centuries. Diffraction provides the unique ability to observe these structural changes in fine detail on lengthscales spanning atomic to nanometre dimensions. Amongst the broad suite of diffraction tools available today, neutrons provide unique capabilities of fundamental importance. However, to date, the growth of neutron diffraction under extremes of pressure has been limited by the weakness of available sources. In recent years, substantial government investments have led to the construction of a new generation of neutron sources while existing facilities have been revitalized by upgrades. The timely convergence of these bright facilities with new pressure-cell technologies suggests that the field of high-pressure (HP) neutron science is on the cusp of substantial growth. Here, the history of HP neutron research is examined with the hope of gleaning an accurate prediction of where some of these revolutionary capabilities will lead in the near future. In particular, a dramatic expansion of current pressure-temperature range is likely, with corresponding increased scope for extreme-conditions science with neutron diffraction. This increase in coverage will be matched with improvements in data quality. Furthermore, we can also expect broad new capabilities beyond diffraction, including in neutron imaging, small angle scattering and inelastic spectroscopy.

Large-volume protein crystal growth for neutron macromolecular crystallography

Neutron macromolecular crystallography (NMC) is the prevailing method for the accurate determination of the positions of H atoms in macromolecules. As neutron sources are becoming more available to general users, finding means to optimize the growth of protein crystals to sizes suitable for NMC is extremely important. Historically, much has been learned about growing crystals for X-ray diffraction. However, owing to new-generation synchrotron X-ray facilities and sensitive detectors, protein crystal sizes as small as in the nano-range have become adequate for structure determination, lessening the necessity to grow large crystals. Here, some of the approaches, techniques and considerations for the growth of crystals to significant dimensions that are now relevant to NMC are revisited. These include experimental strategies utilizing solubility diagrams, ripening effects, classical crystallization techniques, microgravity and theoretical considerations.

Neutron scattering techniques and applications in structural biology

Neutron scattering is exquisitely sensitive to the position, concentration, and dynamics of hydrogen atoms in materials and is a powerful tool for the characterization of structure-function and interfacial relationships in biological systems. Modern neutron scattering facilities offer access to a sophisticated, nondestructive suite of instruments for biophysical characterization that provides spatial and dynamic information spanning from Ångstroms to microns and from picoseconds to microseconds, respectively. Applications in structural biology range from the atomic-resolution analysis of individual hydrogen atoms in enzymes through to meso- and macro-scale analysis of complex biological structures, membranes, and assemblies. The large difference in neutron scattering length between hydrogen and deuterium allows contrast variation experiments to be performed and enables H/D isotopic labeling to be used for selective and systematic analysis of the local structure, dynamics, and interactions of multi-component systems. This overview describes the available techniques and summarizes their practical application to the study of biomolecular systems.

Tuning the density profile of surface-grafted hyaluronan and the effect of counter-ions

The present paper investigates the structure and composition of grafted sodium hyaluronan at a solid-liquid interface using neutron reflection. The solvated polymer at the surface could be described with a density profile that decays exponentially towards the bulk solution. The density profile of the polymer varied depending on the deposition protocol. A single-stage deposition resulted in denser polymer layers, while layers created with a two-stage deposition process were more diffuse and had an overall lower density. Despite the diffuse density profile, two-stage deposition leads to a higher surface excess. Addition of calcium ions causes a strong collapse of the sodium hyaluronan chains, increasing the polymer density near the surface. This effect is more pronounced on the sample prepared by two-stage deposition due to the initial less dense profile. This study provides an understanding at a molecular level of how surface functionalization alters the structure and how surface layers respond to changes in calcium ions in the solvent.

Atomic-resolution structural information from scattering experiments on macromolecules in solution

The pair-distance distribution function (PDDF) contains all structural information probed in an elastic scattering experiment of macromolecular solutions. However, in small-angle x-ray scattering (SAXS) or small-angle neutron scattering (SANS) experiments only their Fourier transform is measured over a restricted range of scattering angles. We therefore developed a mathematically simple and computationally efficient method to calculate the PDDFs as well as accurate scattering intensities from molecular dynamics simulations. The calculated solution scattering intensities are in excellent agreement with SAXS and wide-angle x-ray scattering (WAXS) experiments for a series of proteins. The corresponding PDDFs are remarkably rich in features reporting on the detailed protein structure. Using an inverse Fourier transform method, most of these features can be recovered if scattering intensities are measured up to a momentum transfer of q≈2-3Å(-1). Our results establish that high-precision solution scattering experiments utilizing x-ray free-electron lasers and third generation synchrotron sources can resolve subnanometer structural detail, well beyond size, shape, and fold.

Phase separation in semidilute aqueous poly(N-isopropylacrylamide) solutions

The phase separation mechanism in semidilute aqueous poly(N-isopropylacrylamide) (PNIPAM) solutions is investigated with small-angle neutron scattering (SANS). The nature of the phase transition is probed in static SANS measurements and with time-dependent SANS measurements after a temperature jump. The observed critical exponents of the phase transition describing the temperature dependence of the Ornstein-Zernike amplitude and correlation length are smaller than values from mean-field theory. Time-dependent SANS measurements show that the specific surface decreases with increasing time after a temperature jump above the phase transition. Thus, the formation of additional hydrogen bonds in the collapsed state is a kinetic effect: A certain fraction of water remains as bound water in the system. Moreover, H-D exchange reactions observed in PNIPAM have to be taken into account.

New developments in the ATSAS program package for small-angle scattering data analysis

New developments in the program package ATSAS (version 2.4) for the processing and analysis of isotropic small-angle X-ray and neutron scattering data are described. They include (i) multiplatform data manipulation and display tools, (ii) programs for automated data processing and calculation of overall parameters, (iii) improved usage of high- and low-resolution models from other structural methods, (iv) new algorithms to build three-dimensional models from weakly interacting oligomeric systems and complexes, and (v) enhanced tools to analyse data from mixtures and flexible systems. The new ATSAS release includes installers for current major platforms (Windows, Linux and Mac OSX) and provides improved indexed user documentation. The web-related developments, including a user discussion forum and a widened online access to run ATSAS programs, are also presented.

Deuterium incorporation in biomass cell wall components by NMR analysis

A commercially available deuterated kale sample was analyzed for deuterium incorporation by ionic liquid solution (2)H and (1)H nuclear magnetic resonance (NMR). This protocol was found to effectively measure the percent deuterium incorporation at 33%, comparable to the 31% value determined by combustion. The solution NMR technique also suggested by a qualitative analysis that deuterium is preferentially incorporated into the carbohydrate components of the kale sample.

Rapid visualization of hydrogen positions in protein neutron crystallographic structures

Neutron crystallography is a powerful technique for experimental visualization of the positions of light atoms, including hydrogen and its isotope deuterium. In recent years, structural biologists have shown increasing interest in the technique as it uniquely complements X-ray crystallographic data by revealing the positions of D atoms in macromolecules. With this regained interest, access to macromolecular neutron crystallography beamlines is becoming a limiting step. In this report, it is shown that a rapid data-collection strategy can be a valuable alternative to longer data-collection times in appropriate cases. Comparison of perdeuterated rubredoxin structures refined against neutron data sets collected over hours and up to 5 d shows that rapid neutron data collection in just 14 h is sufficient to provide the positions of 269 D atoms without ambiguity.

Neutron fibre diffraction studies of amyloid using H2O/D2O isotopic replacement

The first neutron fibre diffraction studies of an amyloid system are presented. The techniques used to prepare the large samples needed are described, as well as the procedures used to isotopically replace H2O in the sample by D2O. The results demonstrate the feasibility of this type of approach for the pursuit of novel structural analyses that will strongly complement X-ray fibre diffraction studies and probe aspects of amyloid structure that to date have remained obscure. The approach is demonstrated using an amyloid form of the peptide NSGAITIG, but is equally applicable for the study of other systems such as Alzheimer's Aβ peptide.

Macromolecular neutron crystallography at the Protein Crystallography Station (PCS)

The Protein Crystallography Station (PCS) at Los Alamos Neutron Science Center is a high-performance beamline that forms the core of a capability for neutron macromolecular structure and function determination. Neutron diffraction is a powerful technique for locating H atoms and can therefore provide unique information about how biological macromolecules function and interact with each other and smaller molecules. Users of the PCS have access to neutron beam time, deuteration facilities, the expression of proteins and the synthesis of substrates with stable isotopes and also support for data reduction and structure analysis. The beamline exploits the pulsed nature of spallation neutrons and a large electronic detector in order to collect wavelength-resolved Laue patterns using all available neutrons in the white beam. The PCS user facility is described and highlights from the user program are presented.

The influence of additives on the nanoscopic dynamics of the phospholipid dimyristoylphosphatidylcholine

The influence of additives on the molecular dynamics of the phospholipid dimyristoylphosphatidylcholine (DMPC) in its fully hydrated liquid crystalline phase was studied. Quasielastic neutron scattering (QENS) was used to detect motions with dimensions of some Ångstroms on two different time scales, namely 60ps and 900ps. The effects of myristic acid, farnesol, cholesterol, and sodium glycocholate could consistently be explained on the basis of collective, flow-like motions of the phospholipid molecules. The influence of the additives on these motions was explained by packing effects, corresponding to the reduction of free volume. Cholesterol was found to decrease the mobility of DMPC seen on the 900ps time scale with increasing cholesterol content. In contrast, all other studied additives have no significant effect on the mobility.

Neutron optical beam splitter from holographically structured nanoparticle-polymer composites

We report a breakthrough in the search for versatile diffractive elements for cold neutrons. Nanoparticles are spatially arranged by holographical means in a photopolymer. These grating structures show remarkably efficient diffraction of cold neutrons up to about 50% for effective thicknesses of only 200   μm. They open up a profound perspective for next generation neutron-optical devices with the capability to tune or modulate the neutron diffraction efficiency.

Applications of neutron and X-ray scattering to the study of biologically relevant model membranes

Scattering techniques, in particular electron, neutron and X-ray scattering have played a major role in elucidating the static and dynamic structure of biologically relevant membranes. Importantly, neutron and X-ray scattering have evolved to address new sample preparations that better mimic biological membranes. In this review, we will report on some of the latest model membrane results, and the neutron and X-ray techniques that were used to obtain them.

Protein dynamics investigated by neutron scattering

This contribution describes incoherent quasielastic neutron scattering (QENS) as a suitable tool for investigations of protein dynamics with special emphasis on applications in photosynthesis research. QENS characterizes protein dynamics via the measurement of energy and momentum exchange between sample system and incident low-energy neutrons (1 meV<E<20 meV). This method is especially sensitive for picosecond motions of hydrogen atoms because it makes use of the exceptionally large incoherent neutron scattering cross section of protons and their almost homogeneous distribution in proteins. After a short introduction into the basic principles of neutron scattering, a more detailed description of QENS will be presented including a short overview on instrumentation and theory. Recent QENS results will be discussed for the antenna complex LHC II and PS II membrane fragments. It is shown that diffusive protein dynamics is indispensable for enabling Q(A)(-·) reoxidation by Q(B) at temperatures above 240 K, which explains the strong dependence of this electron transfer step on temperature and hydration level of the sample. Finally, a new laser-QENS pump-probe technique will be introduced which permits in situ monitoring of protein dynamics correlated with a change of the functional state of the sample, i.e. a direct observation of structure-dynamics-function relationships in real time.

Neutrons for biologists: a beginner's guide, or why you should consider using neutrons

From the structures of isolated protein complexes to the molecular dynamics of whole cells, neutron methods can achieve a resolution in complex systems that is inaccessible to other techniques. Biology is fortunate in that it is rich in water and hydrogen, and this allows us to exploit the differential sensitivity of neutrons to this element and its major isotope, deuterium. Furthermore, neutrons exhibit wave properties that allow us to use them in similar ways to light, X-rays and electrons. This review aims to explain the basics of biological neutron science to encourage its greater use in solving difficult problems in the life sciences.

Generalized X-ray and neutron crystallographic analysis: more accurate and complete structures for biological macromolecules

X-ray and neutron crystallographic techniques provide complementary information on the structure and function of biological macromolecules. X-ray and neutron (XN) crystallographic data have been combined in a joint structure-refinement procedure that has been developed using recent advances in modern computational methodologies, including cross-validated maximum-likelihood target functions with gradient-based optimization and simulated annealing. The XN approach for complete (including hydrogen) macromolecular structure analysis provides more accurate and complete structures, as demonstrated for diisopropyl fluorophosphatase, photoactive yellow protein and human aldose reductase. Furthermore, this method has several practical advantages, including the easier determination of the orientation of water molecules, hydroxyl groups and some amino-acid side chains.

A preliminary neutron crystallographic study of an A-DNA crystal

The LADI-III diffractometer at the Institut Laue-Langevin has been used to carry out a preliminary neutron crystallographic study of the self-complementary DNA oligonucleotide d(AGGGGCCCCT)(2) in the A conformation. The results demonstrate the viability of a full neutron crystallographic analysis with the aim of providing enhanced information on the ion-water networks that are known to be important in stabilizing A-DNA. This is the first account of a single-crystal neutron diffraction study of A-DNA. The study was carried out with the smallest crystal used to date for a neutron crystallographic study of a biological macromolecule.

Neutron crystallography: opportunities, challenges, and limitations

Neutron crystallography has had an important, but relatively small role in structural biology over the years. In this review of recently determined neutron structures, a theme emerges of a field currently expanding beyond its traditional boundaries, to address larger and more complex problems, with smaller samples and shorter data collection times, and employing more sophisticated structure determination and refinement methods. The origin of this transformation can be found in a number of advances including first, the development of neutron image-plates and quasi-Laue methods at nuclear reactor neutron sources and the development of time-of-flight Laue methods and electronic detectors at spallation neutron sources; second, new facilities and methods for sample perdeuteration and crystallization; third, new approaches and computational tools for structure determination.